Miller School Scientists Reveal Mechanisms Behind Gene Expression in Mitochondria
Article Summary
- A Miller School research team became the first to map how mitochondrial messenger RNA folds in human cells.
- The expression of DNA involves its transcription into RNA, which is then translated into proteins known as ribosomes.
- The work defines a critical layer of mitochondrial gene expression regulation and may help identify therapeutic targets for neurodegenerative diseases.
A molecular biology research team at the University of Miami Miller School of Medicine has become the first to map out how mitochondrial messenger RNA folds in human cells.
The research advances knowledge about the expression of genes in the mitochondria and paves the way for identification of therapeutic targets for mitochondrial neurodegenerative diseases.
“Dysfunctional mitochondria can cause devastating diseases, frequently with childhood-onset, known as mitochondrial encephalomyopathies. Despite advances in identifying genes responsible for these disorders, their pathophysiological mechanisms have been poorly understood,” said Antoni Barrientos, Ph.D., professor of neurology and biochemistry and molecular biology at the Miller School. “This was partly due to a lack of a full understanding of mitochondrial gene expression. Specifically, nothing was known about how mitochondrial messenger RNA folds and how that could influence its stability and translation in health and disease.”
Now, in a paper published in the July 19 issue of the journal Science, Dr. Barrientos and his coauthors have revealed the structurome of mitochondrial messenger RNA. The research was led by Dr. Barrientos and Flavia Fontanesi, Ph.D., assistant professor of biochemistry and molecular biology at the Miller School, along with their colleague, Silvi Rouskin, Ph.D., assistant professor of microbiology at Harvard Medical School.
Mitochondrial mRNA
Mitochondria are like tiny power plants inside human cells. They convert the nutrients people eat into energy by using oxygen to fuel chemical reactions. Owing to their bacterial origin, mitochondria contain a small, circular DNA that encodes 13 proteins that are components of the enzymes required for energy transduction. All other mitochondrial proteins, up to about 1,500, are encoded in the DNA housed in the nucleus, the cell’s primary repository for DNA.
The expression of DNA involves its transcription into RNA, which is then translated into proteins by molecular machines known as ribosomes. All proteins encoded in the nucleus are synthesized in ribosomes located in the cell’s cytosol. The 13 proteins encoded in the mitochondrial genome are synthesized in specialized ribosomes located within mitochondria. In both cases, a type of RNA known as messenger RNA (mRNA) carries the instructions from DNA to the ribosomes to make proteins.
The way mRNA in the nucleus folds itself up is critical for normal cellular function. Aberrantly folded mRNA causes or contributes to neurological and neurodegenerative diseases. However, the folding of mRNA had never been explored in the context of mitochondrial mRNAs (mt-mRNAs) and mitochondrial diseases.
Dr. Barrientos and his team resolved the folding of the mt-mRNAs while studying Leigh syndrome, a genetic, mitochondrial disease that causes specific cells in the central nervous system to degenerate.
“We wanted to study a mitochondrial disease known as Leigh syndrome, specifically its French-Canadian form that results from mutations in the leucine-rich pentatricopeptide repeat containing (LRPPRC) protein. LRPPRC, encoded in the nuclear genome, is a pivotal regulator of mt-mRNA stability and translation into proteins,” Dr. Barrientos said. “The disease is devastating because infants rarely survive their second year. Now, we have uncovered several basic mechanisms involving mt-mRNA folding that drive pediatric mitochondrial disease, including Leigh syndrome.”
Messenger RNA Folding
To start closing the knowledge gap on mt-mRNA folding, Dr. Barrientos and team used an interdisciplinary approach involving studies on mitochondrial gene expression in health and disease, the development of methods to decipher the structures of all mitochondrial mRNAs, structure-function studies and identification of potential therapeutic targets.
The team devised the mitochondrial dimethyl sulfate mutational profiling with sequencing (mito DMS-MaPseq) method and applied detection of RNA folding ensembles using expectation-maximization (DREEM) clustering to unravel the native mitochondrial messenger RNA (mt-mRNA) folding landscape or structurome in wild-type and LRPPRC–deficient cells, as a model of Leigh syndrome.
The findings helped elucidate LRPPRC’s role as a holdase chaperone that contributes to maintaining mt-mRNA folding and efficient translation. Furthermore, mt-mRNA structural insights in wild-type mitochondria, coupled with biochemical experiments, unveil an array of unique mRNA-programmed translation regulation mechanisms.
The mt-mRNA folding maps provided in this work represent the groundwork for a comprehensive understanding of the relationships between mRNA structure and its stability, processing or translation.
What’s Next?
The team’s work has opened new avenues for scientific exploration.
“The data in the paper define a critical layer of mitochondrial gene expression regulation,” said Dr. Fontanesi. “These mt-mRNA folding maps provide a reference for studying mt-mRNA structures in diverse physiological and pathological contexts.”
The team is continuing to study how mt-mRNA structure adapts to varying cellular contexts, metabolic states and environmental conditions in health and mitochondrial disease.
Dr. Barrientos and Dr. Fontanesi co-mentored J. Conor Moran, an M.D./Ph.D. student in the Department of Biochemistry and Molecular Biology and first author of the study, together with Amir Brivanlou, a graduate student in Dr. Rouskin’s lab.
In Miami, the project was contributed to and is now continued by Michele Brischigliaro, Ph.D., a postdoctoral trainee in Dr. Barrientos’ laboratory.
“Conor was a driving force of the project, bridging the biochemistry performed in our lab and the bioinformatics pipelines developed in the lab of Dr. Rouskin at Harvard,” said Dr. Fontanesi.
Tags: biochemistry and molecular biology, DNA, Dr. Antoni Barrientos, Dr. Flavia Fontanesi, mRNA